Apple growers in Hastings and Napier fear the Ministry for Primary Industries will set the industry back a decade with an order to destroy thousands of imported plants.
However, the ministry believes the American imports still pose an "unacceptable risk".
A group of five growers from across the country have joined together to challenge last week's directive by the Ministry for Primary Industries (MPI) for nurseries and orchardists to contain and/or destroy tens of thousands of apple (Mali's) and stonefruit (Prunus) plants.
The group lodged a Judicial Review with the High Court in Wellington on Friday. August 3, seeking to overturn the MPI decision to destroy plants from a quarantine centre at Washington State University.
The centre has been providing plant material to New Zealand since the 1980s and is the main source of plant material and plant varieties for New Zealand's stonefruit orchards, said Kerry Sixtus, owner of Pattullo's Nurseries Limited in Napier.
The MPI directive includes original plant materials imported between 2012 and 2017, and extends to budwood and propagated materials derived from the original plants, he said.
The order affects 32 orchardists, nurseries, importers and intellectual property companies in Hawke's Bay, Waikato, Nelson and Central Otago.
"As MPI representatives have stated, the MPI directive is based on a paperwork issue. MPI has not provided any evidence of an actual biosecurity risk presented by the relevant plant material," said Sixtus.
"MPI's actions and directives are not based on an adequate assessment of risk. A reactive decision based on MPI's procedural failure will set the industry back 10 to 15 years and cost New Zealand dearly.
"This decision by MPI is likely to result in hundreds of millions of dollars of loss to orchardists and nurseries, and will have a significant effect on the economy."
In total there are 32 different Hawke's Bay parties affected, including orchardists, nurseries and importers involved with the apple, apricot, peach, plum, Nectarine and cherry industries.
MPI's action also threatened to burn a new variety of apple being developed by the Yummy Fruit Company in Hastings, who planted the imported trees six years ago.
"Progress is going to go up in flames," general manager Paul Paynter said.
"We're losing the future of our industry really, all these varieties are the latest and greatest things that excite the consumer. Biosecurity absolutely is paramount, but we're talking six years of history. Some of this has been planted quite a few years ago and has been blooming and pruned for several years now.
"If there was a horse, the horse has bolted in terms of deceases. Burning them now won't help. The horse has bolted - it's done five laps of the track, been put out to pasture and turned into dog food, it's that long after the event."
It was unlikely any serious diseases would develop now, he said.
Responding to the action, a MPI spokesperson said the ministry was confident with its decisions and the processes it had followed.
"We understand this is difficult for affected growers, nurseries and importers.
"We have carefully assessed all of the risks associated with this plant material. Our decisions are about protecting New Zealand and our wider horticultural industry from biosecurity risks."
MPI was unable to comment further because the matter was before the courts but last week it announced it was taking action to protect New Zealand from potential biosecurity risk after an audit found significant failures at an overseas facility screening apple and stonefruit cuttings.
MPI on its website said a routine audit in March found several critical non-compliances at the Clean Plant Centre Northwest at Washington State University.
"The audit showed we can have little confidence in the testing carried out by the facility.
"There were a number of failures to undertake the required testing, as well as incorrect reporting of results, and missing records. Two tests were recorded as negative ... but later recorded as positive, yet MPI was not informed.
"At MPI's request, US authorities had conducted an investigation which had since confirmed these findings."
A two day hearing would take place on Thursday, August 16.